\section{NFcore::DORRxnClass Class Reference}
\label{classNFcore_1_1DORRxnClass}\index{NFcore::DORRxnClass@{NFcore::DORRxnClass}}
{\tt \#include $<$reaction.hh$>$}

Inheritance diagram for NFcore::DORRxnClass::\begin{figure}[H]
\begin{center}
\leavevmode
\includegraphics[height=2cm]{classNFcore_1_1DORRxnClass}
\end{center}
\end{figure}
\subsection*{Public Member Functions}
\begin{CompactItemize}
\item 
{\bf DORRxnClass} (string {\bf name}, double {\bf baseRate}, {\bf TransformationSet} $\ast${\bf transformationSet}, vector$<$ {\bf LocalFunction} $\ast$ $>$ \&{\bf lfList}, vector$<$ string $>$ \&lfArgumentPointerNameList)
\item 
virtual {\bf $\sim$DORRxnClass} ()
\item 
virtual void {\bf init} ()
\item 
virtual void {\bf prepareForSimulation} ()
\item 
virtual bool {\bf tryToAdd} ({\bf Molecule} $\ast$m, unsigned int reactantPos)
\item 
virtual void {\bf remove} ({\bf Molecule} $\ast$m, unsigned int reactantPos)
\item 
virtual double {\bf update\_\-a} ()
\item 
virtual int {\bf getDORreactantPosition} () const 
\item 
virtual void {\bf notifyRateFactorChange} ({\bf Molecule} $\ast$m, int reactantIndex, int rxnListIndex)
\item 
virtual unsigned int {\bf getReactantCount} (unsigned int reactantIndex) const 
\item 
virtual void {\bf printDetails} () const 
\item 
virtual void {\bf printFullDetails} () const 
\item 
void {\bf directAddForDebugging} ({\bf Molecule} $\ast$m)
\item 
void {\bf printTreeForDebugging} ()
\end{CompactItemize}
\subsection*{Static Public Member Functions}
\begin{CompactItemize}
\item 
static void {\bf test1} ({\bf System} $\ast$s)
\end{CompactItemize}
\subsection*{Protected Member Functions}
\begin{CompactItemize}
\item 
virtual double {\bf evaluateLocalFunctions} ({\bf MappingSet} $\ast${\bf ms})
\item 
virtual void {\bf pickMappingSets} (double randNumber) const 
\end{CompactItemize}
\subsection*{Protected Attributes}
\begin{CompactItemize}
\item 
{\bf ReactantList} $\ast$$\ast$ {\bf reactantLists}
\item 
{\bf ReactantTree} $\ast$ {\bf reactantTree}
\item 
{\bf MappingSet} $\ast$ {\bf ms}
\item 
int {\bf DORreactantIndex}
\item 
vector$<$ {\bf LocalFunction} $\ast$ $>$ {\bf lfList}
\item 
vector$<$ int $>$ {\bf indexIntoMappingSet}
\item 
vector$<$ double $>$ {\bf localFunctionValue}
\end{CompactItemize}


\subsection{Constructor \& Destructor Documentation}
\index{NFcore::DORRxnClass@{NFcore::DORRxnClass}!DORRxnClass@{DORRxnClass}}
\index{DORRxnClass@{DORRxnClass}!NFcore::DORRxnClass@{NFcore::DORRxnClass}}
\subsubsection{\setlength{\rightskip}{0pt plus 5cm}DORRxnClass::DORRxnClass (string {\em name}, double {\em baseRate}, {\bf TransformationSet} $\ast$ {\em transformationSet}, vector$<$ {\bf LocalFunction} $\ast$ $>$ \& {\em lfList}, vector$<$ string $>$ \& {\em lfArgumentPointerNameList})}\label{classNFcore_1_1DORRxnClass_a3517167125e2042cca91e4342c7053e}




Step 3: Wheh! now we can finally get on the business of creating the reactant lists and the reactant tree and setting the usual reactionClass parameters \index{NFcore::DORRxnClass@{NFcore::DORRxnClass}!$\sim$DORRxnClass@{$\sim$DORRxnClass}}
\index{$\sim$DORRxnClass@{$\sim$DORRxnClass}!NFcore::DORRxnClass@{NFcore::DORRxnClass}}
\subsubsection{\setlength{\rightskip}{0pt plus 5cm}DORRxnClass::$\sim$DORRxnClass ()\hspace{0.3cm}{\tt  [virtual]}}\label{classNFcore_1_1DORRxnClass_7b178d5f4595a551a4da7c64f9678454}




\subsection{Member Function Documentation}
\index{NFcore::DORRxnClass@{NFcore::DORRxnClass}!init@{init}}
\index{init@{init}!NFcore::DORRxnClass@{NFcore::DORRxnClass}}
\subsubsection{\setlength{\rightskip}{0pt plus 5cm}void DORRxnClass::init ()\hspace{0.3cm}{\tt  [virtual]}}\label{classNFcore_1_1DORRxnClass_bd3127e922a51881509c4958e46fc56f}




Implements {\bf NFcore::ReactionClass} \doxyref{}{p.}{classNFcore_1_1ReactionClass_fa3006801b4fcf821358bfca9bab8aa1}.\index{NFcore::DORRxnClass@{NFcore::DORRxnClass}!prepareForSimulation@{prepareForSimulation}}
\index{prepareForSimulation@{prepareForSimulation}!NFcore::DORRxnClass@{NFcore::DORRxnClass}}
\subsubsection{\setlength{\rightskip}{0pt plus 5cm}virtual void NFcore::DORRxnClass::prepareForSimulation ()\hspace{0.3cm}{\tt  [inline, virtual]}}\label{classNFcore_1_1DORRxnClass_afc1267a5cd558075d87f79837b3dcba}




Implements {\bf NFcore::ReactionClass} \doxyref{}{p.}{classNFcore_1_1ReactionClass_f6466927590b894478fbe765f4da8aad}.\index{NFcore::DORRxnClass@{NFcore::DORRxnClass}!tryToAdd@{tryToAdd}}
\index{tryToAdd@{tryToAdd}!NFcore::DORRxnClass@{NFcore::DORRxnClass}}
\subsubsection{\setlength{\rightskip}{0pt plus 5cm}bool DORRxnClass::tryToAdd ({\bf Molecule} $\ast$ {\em m}, unsigned int {\em reactantPos})\hspace{0.3cm}{\tt  [virtual]}}\label{classNFcore_1_1DORRxnClass_d766aeb571ab65fc188ef9fea8212384}




Implements {\bf NFcore::ReactionClass} \doxyref{}{p.}{classNFcore_1_1ReactionClass_7ef57431ab858d1039e9efedd011f1f0}.\index{NFcore::DORRxnClass@{NFcore::DORRxnClass}!remove@{remove}}
\index{remove@{remove}!NFcore::DORRxnClass@{NFcore::DORRxnClass}}
\subsubsection{\setlength{\rightskip}{0pt plus 5cm}virtual void NFcore::DORRxnClass::remove ({\bf Molecule} $\ast$ {\em m}, unsigned int {\em reactantPos})\hspace{0.3cm}{\tt  [inline, virtual]}}\label{classNFcore_1_1DORRxnClass_91f26bc79e9d4b754139b9f58abcc484}




Implements {\bf NFcore::ReactionClass} \doxyref{}{p.}{classNFcore_1_1ReactionClass_e9f356905524d6e370059b1e4ef5754a}.\index{NFcore::DORRxnClass@{NFcore::DORRxnClass}!update\_\-a@{update\_\-a}}
\index{update\_\-a@{update\_\-a}!NFcore::DORRxnClass@{NFcore::DORRxnClass}}
\subsubsection{\setlength{\rightskip}{0pt plus 5cm}double DORRxnClass::update\_\-a ()\hspace{0.3cm}{\tt  [virtual]}}\label{classNFcore_1_1DORRxnClass_077d5dc28b205d46a14d22487c08bb7e}




Implements {\bf NFcore::ReactionClass} \doxyref{}{p.}{classNFcore_1_1ReactionClass_f5aed18705e78d14bd1a8f82068add70}.\index{NFcore::DORRxnClass@{NFcore::DORRxnClass}!getDORreactantPosition@{getDORreactantPosition}}
\index{getDORreactantPosition@{getDORreactantPosition}!NFcore::DORRxnClass@{NFcore::DORRxnClass}}
\subsubsection{\setlength{\rightskip}{0pt plus 5cm}virtual int NFcore::DORRxnClass::getDORreactantPosition () const\hspace{0.3cm}{\tt  [inline, virtual]}}\label{classNFcore_1_1DORRxnClass_2a1fbaba84429f5b076ce40e1848cb65}




Reimplemented from {\bf NFcore::ReactionClass} \doxyref{}{p.}{classNFcore_1_1ReactionClass_06f85ae28c934c344542626c627929e7}.\index{NFcore::DORRxnClass@{NFcore::DORRxnClass}!notifyRateFactorChange@{notifyRateFactorChange}}
\index{notifyRateFactorChange@{notifyRateFactorChange}!NFcore::DORRxnClass@{NFcore::DORRxnClass}}
\subsubsection{\setlength{\rightskip}{0pt plus 5cm}void DORRxnClass::notifyRateFactorChange ({\bf Molecule} $\ast$ {\em m}, int {\em reactantIndex}, int {\em rxnListIndex})\hspace{0.3cm}{\tt  [virtual]}}\label{classNFcore_1_1DORRxnClass_ef4d5b83d7f268142af4bbb6c13f89b3}




Implements {\bf NFcore::ReactionClass} \doxyref{}{p.}{classNFcore_1_1ReactionClass_c18b82dc36c68699c00802201d7745cd}.\index{NFcore::DORRxnClass@{NFcore::DORRxnClass}!getReactantCount@{getReactantCount}}
\index{getReactantCount@{getReactantCount}!NFcore::DORRxnClass@{NFcore::DORRxnClass}}
\subsubsection{\setlength{\rightskip}{0pt plus 5cm}unsigned int DORRxnClass::getReactantCount (unsigned int {\em reactantIndex}) const\hspace{0.3cm}{\tt  [virtual]}}\label{classNFcore_1_1DORRxnClass_bff81c460e3398249e095f1f52a60652}




Implements {\bf NFcore::ReactionClass} \doxyref{}{p.}{classNFcore_1_1ReactionClass_a39fd321f4d58d79fa72812d65f1c762}.\index{NFcore::DORRxnClass@{NFcore::DORRxnClass}!printDetails@{printDetails}}
\index{printDetails@{printDetails}!NFcore::DORRxnClass@{NFcore::DORRxnClass}}
\subsubsection{\setlength{\rightskip}{0pt plus 5cm}void DORRxnClass::printDetails () const\hspace{0.3cm}{\tt  [virtual]}}\label{classNFcore_1_1DORRxnClass_9d90ba3fc8f0effd97f14080ed76b608}




Reimplemented from {\bf NFcore::ReactionClass} \doxyref{}{p.}{classNFcore_1_1ReactionClass_7944db14780627ea05cf290688a8bfd3}.\index{NFcore::DORRxnClass@{NFcore::DORRxnClass}!printFullDetails@{printFullDetails}}
\index{printFullDetails@{printFullDetails}!NFcore::DORRxnClass@{NFcore::DORRxnClass}}
\subsubsection{\setlength{\rightskip}{0pt plus 5cm}virtual void NFcore::DORRxnClass::printFullDetails () const\hspace{0.3cm}{\tt  [inline, virtual]}}\label{classNFcore_1_1DORRxnClass_25114f968aea64b0ba990ce58b974fb5}




Implements {\bf NFcore::ReactionClass} \doxyref{}{p.}{classNFcore_1_1ReactionClass_521a0b7a474568522bec973cfa6b5242}.\index{NFcore::DORRxnClass@{NFcore::DORRxnClass}!directAddForDebugging@{directAddForDebugging}}
\index{directAddForDebugging@{directAddForDebugging}!NFcore::DORRxnClass@{NFcore::DORRxnClass}}
\subsubsection{\setlength{\rightskip}{0pt plus 5cm}void NFcore::DORRxnClass::directAddForDebugging ({\bf Molecule} $\ast$ {\em m})}\label{classNFcore_1_1DORRxnClass_2d6fa883d31905b2206d13a4645c5d16}


\index{NFcore::DORRxnClass@{NFcore::DORRxnClass}!printTreeForDebugging@{printTreeForDebugging}}
\index{printTreeForDebugging@{printTreeForDebugging}!NFcore::DORRxnClass@{NFcore::DORRxnClass}}
\subsubsection{\setlength{\rightskip}{0pt plus 5cm}void NFcore::DORRxnClass::printTreeForDebugging ()}\label{classNFcore_1_1DORRxnClass_28618d0587e8a45d9d1cb1d0386018be}


\index{NFcore::DORRxnClass@{NFcore::DORRxnClass}!test1@{test1}}
\index{test1@{test1}!NFcore::DORRxnClass@{NFcore::DORRxnClass}}
\subsubsection{\setlength{\rightskip}{0pt plus 5cm}void DORRxnClass::test1 ({\bf System} $\ast$ {\em s})\hspace{0.3cm}{\tt  [static]}}\label{classNFcore_1_1DORRxnClass_93f985d32abf0195ab250f8b6a33c997}


\index{NFcore::DORRxnClass@{NFcore::DORRxnClass}!evaluateLocalFunctions@{evaluateLocalFunctions}}
\index{evaluateLocalFunctions@{evaluateLocalFunctions}!NFcore::DORRxnClass@{NFcore::DORRxnClass}}
\subsubsection{\setlength{\rightskip}{0pt plus 5cm}double DORRxnClass::evaluateLocalFunctions ({\bf MappingSet} $\ast$ {\em ms})\hspace{0.3cm}{\tt  [protected, virtual]}}\label{classNFcore_1_1DORRxnClass_be0c6a9d9313d5ab383056373993c315}


\index{NFcore::DORRxnClass@{NFcore::DORRxnClass}!pickMappingSets@{pickMappingSets}}
\index{pickMappingSets@{pickMappingSets}!NFcore::DORRxnClass@{NFcore::DORRxnClass}}
\subsubsection{\setlength{\rightskip}{0pt plus 5cm}void DORRxnClass::pickMappingSets (double {\em randNumber}) const\hspace{0.3cm}{\tt  [protected, virtual]}}\label{classNFcore_1_1DORRxnClass_5d5d078d2a84602132b708a9bcfb078f}




Implements {\bf NFcore::ReactionClass} \doxyref{}{p.}{classNFcore_1_1ReactionClass_ff3336a876f9e81904ee2b7be86bbdc5}.

\subsection{Member Data Documentation}
\index{NFcore::DORRxnClass@{NFcore::DORRxnClass}!reactantLists@{reactantLists}}
\index{reactantLists@{reactantLists}!NFcore::DORRxnClass@{NFcore::DORRxnClass}}
\subsubsection{\setlength{\rightskip}{0pt plus 5cm}{\bf ReactantList}$\ast$$\ast$ {\bf NFcore::DORRxnClass::reactantLists}\hspace{0.3cm}{\tt  [protected]}}\label{classNFcore_1_1DORRxnClass_3bf2edf9e3727570ed40bd78981a436d}


\index{NFcore::DORRxnClass@{NFcore::DORRxnClass}!reactantTree@{reactantTree}}
\index{reactantTree@{reactantTree}!NFcore::DORRxnClass@{NFcore::DORRxnClass}}
\subsubsection{\setlength{\rightskip}{0pt plus 5cm}{\bf ReactantTree}$\ast$ {\bf NFcore::DORRxnClass::reactantTree}\hspace{0.3cm}{\tt  [protected]}}\label{classNFcore_1_1DORRxnClass_0092e4152b63564ac4bdbe7483f75ee9}


\index{NFcore::DORRxnClass@{NFcore::DORRxnClass}!ms@{ms}}
\index{ms@{ms}!NFcore::DORRxnClass@{NFcore::DORRxnClass}}
\subsubsection{\setlength{\rightskip}{0pt plus 5cm}{\bf MappingSet}$\ast$ {\bf NFcore::DORRxnClass::ms}\hspace{0.3cm}{\tt  [protected]}}\label{classNFcore_1_1DORRxnClass_aa697478dd241353c26cb95cab98465d}


\index{NFcore::DORRxnClass@{NFcore::DORRxnClass}!DORreactantIndex@{DORreactantIndex}}
\index{DORreactantIndex@{DORreactantIndex}!NFcore::DORRxnClass@{NFcore::DORRxnClass}}
\subsubsection{\setlength{\rightskip}{0pt plus 5cm}int {\bf NFcore::DORRxnClass::DORreactantIndex}\hspace{0.3cm}{\tt  [protected]}}\label{classNFcore_1_1DORRxnClass_093d9bdb7894f01306b18e7106c5401e}


\index{NFcore::DORRxnClass@{NFcore::DORRxnClass}!lfList@{lfList}}
\index{lfList@{lfList}!NFcore::DORRxnClass@{NFcore::DORRxnClass}}
\subsubsection{\setlength{\rightskip}{0pt plus 5cm}vector$<${\bf LocalFunction} $\ast$$>$ {\bf NFcore::DORRxnClass::lfList}\hspace{0.3cm}{\tt  [protected]}}\label{classNFcore_1_1DORRxnClass_6e9f3fa8bea0187001b8453644968a6b}


\index{NFcore::DORRxnClass@{NFcore::DORRxnClass}!indexIntoMappingSet@{indexIntoMappingSet}}
\index{indexIntoMappingSet@{indexIntoMappingSet}!NFcore::DORRxnClass@{NFcore::DORRxnClass}}
\subsubsection{\setlength{\rightskip}{0pt plus 5cm}vector$<$int$>$ {\bf NFcore::DORRxnClass::indexIntoMappingSet}\hspace{0.3cm}{\tt  [protected]}}\label{classNFcore_1_1DORRxnClass_bc0c15a43a0d34452de57bfa506b6c66}


\index{NFcore::DORRxnClass@{NFcore::DORRxnClass}!localFunctionValue@{localFunctionValue}}
\index{localFunctionValue@{localFunctionValue}!NFcore::DORRxnClass@{NFcore::DORRxnClass}}
\subsubsection{\setlength{\rightskip}{0pt plus 5cm}vector$<$double$>$ {\bf NFcore::DORRxnClass::localFunctionValue}\hspace{0.3cm}{\tt  [protected]}}\label{classNFcore_1_1DORRxnClass_9da1ed7afc05d59b0c24f859b30c54d3}




The documentation for this class was generated from the following files:\begin{CompactItemize}
\item 
/home/msneddon/eclipse/ganymede\_\-cpp/workspace/NFsim\_\-svn/src/NFreactions/reactions/{\bf reaction.hh}\item 
/home/msneddon/eclipse/ganymede\_\-cpp/workspace/NFsim\_\-svn/src/NFreactions/reactions/{\bf DORreaction.cpp}\end{CompactItemize}
